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Knowledge of plant recognition of insects is largely limited to a few resistance (R) genes against sap‐sucking insects. Hypersensitive response (HR) characterizes monogenic plant traits relying on R genes in several pathosystems. HR‐like cell death can be triggered by eggs of cabbage white butterflies (Pieris spp.), pests of cabbage crops (Brassica spp.), reducing egg survival and representing an effective plant resistance trait before feeding damage occurs. Here, we performed genetic mapping of HR‐like cell death induced by Pieris brassicae eggs in the black mustard Brassica nigra (B. nigra). We show that HR‐like cell death segregates as a Mendelian trait and identified a single dominant locus on chromosome B3, named PEK (Pieris egg‐ killing). Eleven genes are located in an approximately 50 kb region, including a cluster of genes encoding intracellular TIR‐NBS‐LRR (TNL) receptor proteins. The PEK locus is highly polymorphic between the parental accessions of our mapping populations and among B. nigra reference genomes. Our study is the first one to identify a single locus potentially involved in HR‐like cell death induced by insect eggs in B. nigra. Further fine‐mapping, comparative genomics and validation of the PEK locus will shed light on the role of these TNL receptors in egg‐killing HR. Summary statement: Hypersensitive response induced by cabbage white butterfly eggs in Brassica spp. reduces survival and represents an effective plant resistance trait. For the first time, a single dominant locus was identified in the wild crucifer Brassica nigra, which contains a cluster of genes encoding intracellular TIR‐NBS‐LRR (TNLs) receptors. [ABSTRACT FROM AUTHOR]

Research on C4 and C3‐C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of these traits will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3‐C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify orthology levels using synteny maps between all pairs of taxa, (iii) ⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠⁠describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3‐C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the sampling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high‐quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome‐based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3‐C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea. Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3‐C4 intermediate photosynthesis. Summary statement: The established high‐quality de novo genome assemblies for 19 taxa of the Brassiceae tribe provide the basis for genetics approaches unravelling C3‐C4 intermediate photosynthesis. [ABSTRACT FROM AUTHOR]

SUMMARY: Lactuca saligna L. is a wild relative of cultivated lettuce (Lactuca sativa L.), with which it is partially interfertile. Hybrid progeny suffer from hybrid incompatibility (HI), resulting in reduced fertility and distorted transmission ratios. Lactuca saligna displays broad‐spectrum resistance against lettuce downy mildew caused by Bremia lactucae Regel and is considered a non‐host species. This phenomenon of resistance in L. saligna is called non‐host resistance (NHR). One possible mechanism behind this NHR is through the plant–pathogen interaction triggered by pathogen recognition receptors, including nucleotide‐binding leucine‐rich repeat (NLR) proteins and receptor‐like kinases (RLKs). We report a chromosome‐level genome assembly of L. saligna (accession CGN05327), leading to the identification of two large paracentric inversions (>50 Mb) between L. saligna and L. sativa. Genome‐wide searches delineated the major resistance clusters as regions enriched in NLRs and RLKs. Three of the enriched regions co‐locate with previously identified NHR intervals. RNA‐seq analysis of Bremia‐infected lettuce identified several differentially expressed RLKs in NHR regions. Three tandem wall‐associated kinase‐encoding genes (WAKs) in the NHR8 interval display particularly high expression changes at an early stage of infection. We propose RLKs as strong candidates for determinants of the NHR phenotype of L. saligna. Significance Statement: We sequenced and analyzed the genome of the wild lettuce Lactuca saligna, which is resistant against lettuce downy mildew. We analyzed its population diversity and genetic variation, especially focusing on resistance genes and hybrid compatibility. Our results suggest new targets from L. saligna for future resistance breeding in lettuce. [ABSTRACT FROM AUTHOR]

SUMMARY: Photosynthesis is a key process in sustaining plant and human life. Improving the photosynthetic capacity of agricultural crops is an attractive means to increase their yields. While the core mechanisms of photosynthesis are highly conserved in C3 plants, these mechanisms are very flexible, allowing considerable diversity in photosynthetic properties. Among this diversity is the maintenance of high photosynthetic light‐use efficiency at high irradiance as identified in a small number of exceptional C3 species. Hirschfeldia incana, a member of the Brassicaceae family, is such an exceptional species, and because it is easy to grow, it is an excellent model for studying the genetic and physiological basis of this trait. Here, we present a reference genome of H. incana and confirm its high photosynthetic light‐use efficiency. While H. incana has the highest photosynthetic rates found so far in the Brassicaceae, the light‐saturated assimilation rates of closely related Brassica rapa and Brassica nigra are also high. The H. incana genome has extensively diversified from that of B. rapa and B. nigra through large chromosomal rearrangements, species‐specific transposon activity, and differential retention of duplicated genes. Duplicated genes in H. incana, B. rapa, and B. nigra that are involved in photosynthesis and/or photoprotection show a positive correlation between copy number and gene expression, providing leads into the mechanisms underlying the high photosynthetic efficiency of these species. Our work demonstrates that the H. incana genome serves as a valuable resource for studying the evolution of high photosynthetic light‐use efficiency and enhancing photosynthetic rates in crop species. Significance Statement: Hirschfeldia incana is a diploid, wild species, closely related to Brassica crops, which displays remarkably high photosynthesis rates at high irradiance, a desirable trait to improve in crops to increase yield. We propose H. incana as an attractive high‐photosynthesis model species and present the reference genome sequence as a valuable resource for studying the evolution, genetics, and physiology of high photosynthetic light‐use efficiency at high irradiances. [ABSTRACT FROM AUTHOR]

Polyphagous insects often show specialization in feeding on different host plants in terms of survival and growth and, therefore, can be considered minor or major pests of particular hosts. Whether polyphagous insects employ a common transcriptional response to cope with defenses from diverse host plants is under‐studied. We focused on patterns of transcriptional plasticity in polyphagous moths (Noctuidae), of which many species are notorious pests, in relation to herbivore performance on different host plants. We compared the transcriptional plasticity of five polyphagous moth species feeding and developing on three different host plant species. Using a comparative phylogenetic framework, we evaluated if successful herbivory, as measured by larval performance, is determined by a shared or lineage‐specific transcriptional response. The upregulated transcriptional activity, or gene expression pattern, of larvae feeding on the different host plants and artificial control diet was highly plastic and moth species‐specific. Specialization, defined as high herbivore success for specific host plants, was not generally linked to a lower number of induced genes. Moths that were more distantly related and showing high herbivore success for certain host plants showed shared expression of multiple homologous genes, indicating convergence. We further observed specific transcriptional responses within phylogenetic lineages. These expression patterns for specific host plant species are likely caused by shared evolutionary histories, for example, symplesiomorphic patterns, and could therefore not be associated with herbivore success alone. Multiple gene families, with roles in plant digestion and detoxification, were widely expressed in response to host plant feeding but again showed highly moth species‐specific. Consequently, high herbivore success for specific host plants is also driven by species‐specific transcriptional plasticity. Thus, potential pest moths display a complex and species‐specific transcriptional plasticity. [ABSTRACT FROM AUTHOR]

Summary: Strigolactones (SLs) are rhizosphere signalling molecules and phytohormones. The biosynthetic pathway of SLs in tomato has been partially elucidated, but the structural diversity in tomato SLs predicts that additional biosynthetic steps are required. Here, root RNA‐seq data and co‐expression analysis were used for SL biosynthetic gene discovery.This strategy resulted in a candidate gene list containing several cytochrome P450s. Heterologous expression in Nicotiana benthamiana and yeast showed that one of these, CYP712G1, can catalyse the double oxidation of orobanchol, resulting in the formation of three didehydro‐orobanchol (DDH) isomers.Virus‐induced gene silencing and heterologous expression in yeast showed that one of these DDH isomers is converted to solanacol, one of the most abundant SLs in tomato root exudate. Protein modelling and substrate docking analysis suggest that hydroxy‐orbanchol is the likely intermediate in the conversion from orobanchol to the DDH isomers.Phylogenetic analysis demonstrated the occurrence of CYP712G1 homologues in the Eudicots only, which fits with the reports on DDH isomers in that clade. Protein modelling and orobanchol docking of the putative tobacco CYP712G1 homologue suggest that it can convert orobanchol to similar DDH isomers as tomato. [ABSTRACT FROM AUTHOR]

Summary: Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence. [ABSTRACT FROM AUTHOR]

SUMMARY: Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA‐seq libraries and 136 307 full‐length PacBio Iso‐seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At‐α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS‐box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full‐length transcripts related to ABA‐mediated seed dormancy discovered a conserved isoform of PIF6‐β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni‐marburg.de/aetar_db). Significance Statement: Improved gene annotation of Aethionema arabicum using long‐read transcript sequencing provides a plethora of full‐length isoforms and an important resource for Brassicaceae evolution studies. [ABSTRACT FROM AUTHOR]

Summary: Evolutionary arms‐races between plants and insect herbivores have long been proposed to generate key innovations such as plant toxins and detoxification mechanisms that can drive diversification of the interacting species. A novel front‐line of plant defence is the killing of herbivorous insect eggs.We test whether an egg‐killing plant trait has an evolutionary basis in such a plant–insect arms‐race. Within the crucifer family (Brassicaceae), some species express a hypersensitive response (HR)‐like necrosis underneath butterfly eggs (Pieridae) that leads to eggs desiccating or falling off the plant. We studied the phylogenetic distribution of this trait, its egg‐killing effect on and elicitation by butterflies, by screening 31 Brassicales species, and nine Pieridae species.We show a clade‐specific induction of strong, egg‐killing HR‐like necrosis mainly in species of the Brassiceae tribe including Brassica crops and close relatives. The necrosis is strongly elicited by pierid butterflies that are specialists of crucifers. Furthermore, HR‐like necrosis is linked to PR1 defence gene expression, accumulation of reactive oxygen species and cell death, eventually leading to egg‐killing.Our findings suggest that the plants' egg‐killing trait is a new front on the evolutionary arms‐race between Brassicaceae and pierid butterflies beyond the well‐studied plant toxins that have evolved against their caterpillars. [ABSTRACT FROM AUTHOR]

Summary: The APETALA2 (AP2) subfamily of transcription factors are key regulators of angiosperm root, shoot, flower and embryo development. The broad diversity of anatomical and morphological structures is potentially associated with the genomic dynamics of the AP2 subfamily. However, a comprehensive phylogenomic analysis of the AP2 subfamily across angiosperms is lacking. We combined phylogenetic and synteny analysis of distinct AP2 subclades in the completed genomes of 107 angiosperm species. We identified major changes in copy number variation and genomic context within subclades across lineages, and discuss how these changes may have contributed to the evolution of lineage‐specific traits. Multiple AP2 subclades show highly conserved patterns of copy number and synteny across angiosperms, while others are more dynamic and show distinct lineage‐specific patterns. As examples of lineage‐specific morphological divergence due to AP2 subclade dynamics, we hypothesize that loss of PLETHORA1/2 in monocots correlates with the absence of taproots, whereas independent lineage‐specific changes of PLETHORA4/BABY BOOM and WRINKLED1 genes in Brassicaceae and monocots point towards regulatory divergence of embryogenesis between these lineages. Additionally, copy number expansion of TOE1 and TOE3/AP2 in asterids is implicated with differential regulation of flower development. Moreover, we show that the genomic context of AP2s is in general highly specialized per angiosperm lineage. To our knowledge, this study is the first to shed light on the evolutionary divergence of the AP2 subfamily subclades across major angiosperm lineages and emphasizes the need for lineage‐specific characterization of developmental networks to understand trait variability further. [ABSTRACT FROM AUTHOR]

Summary: Plants produce an array of specialized metabolites with important ecological functions. The mechanisms underpinning the evolution of new biosynthetic pathways are not well‐understood. Here, we exploit available genome sequence resources to investigate triterpene biosynthesis across the Brassicaceae.Oxidosqualene cyclases (OSCs) catalyze the first committed step in triterpene biosynthesis. Systematic analysis of 13 sequenced Brassicaceae genomes was performed to identify all OSC genes. The genome neighbourhoods (GNs) around a total of 163 OSC genes were investigated to identify Pfam domains significantly enriched in these regions. All‐vs‐all comparisons of OSC neighbourhoods and phylogenomic analysis were used to investigate the sequence similarity and evolutionary relationships of the numerous candidate triterpene biosynthetic gene clusters (BGCs) observed. Functional analysis of three representative BGCs was carried out and their triterpene pathway products were elucidated.Our results indicate that plant genomes are remarkably plastic, and that dynamic GNs generate new biosynthetic pathways in different Brassicaceae lineages by shuffling the genes encoding a core palette of triterpene‐diversifying enzymes, presumably in response to strong environmental selection pressure.These results illuminate a genomic basis for diversification of plant‐specialized metabolism through natural combinatorics of enzyme families, which can be mimicked using synthetic biology to engineer diverse bioactive molecules. See also the Commentary on this article by Peters, 227: 992–994. [ABSTRACT FROM AUTHOR]

Premise: Whole‐genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. Methods: Phylo‐transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. Results: Well‐supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae‐specific WGD event Th‐ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well‐supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. Conclusions: Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: Previous phylogenetic studies employing molecular markers have yielded various insights into the evolutionary history across Brassicales, but many relationships between families remain poorly supported or unresolved. A recent phylotranscriptomic approach utilizing 1155 nuclear markers obtained robust estimates for relationships among 14 of 17 families. Here we report a complete family‐level phylogeny estimated using the plastid genome. METHODS: We conducted phylogenetic analyses on a concatenated data set comprising 44,926 bp from 72 plastid genes for species distributed across all 17 families. Our analysis includes three additional families, Tovariaceae, Salvadoraceae, and Setchellanthaceae, that were omitted in the previous phylotranscriptomic study. KEY RESULTS: Our phylogenetic analyses obtained fully resolved and strongly supported estimates for all nodes across Brassicales. Importantly, these findings are congruent with the topology reported in the phylotranscriptomic study. This consistency suggests that future studies could utilize plastid genomes as markers for resolving relationships within some notoriously difficult clades across Brassicales. We used this new phylogenetic framework to verify the placement of the At‐α event near the origin of Brassicaceae, with median date estimates of 31.8 to 42.8 million years ago and restrict the At‐β event to one of two nodes with median date estimates between 85 to 92.2 million years ago. These events ultimately gave rise to novel chemical defenses and are associated with subsequent shifts in net diversification rates. CONCLUSIONS: We anticipate that these findings will aid future comparative evolutionary studies across Brassicales, including selecting candidates for whole‐genome sequencing projects. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY:: The Irano‐Turanian region harbors three biodiversity hotspots and ∼25% of Brassicaceae species are endemic to the region. Aethionema (∼61 species) is the sister lineage to the core Brassicaceae and occurs mainly in the Irano‐Turanian region. The evolutionary important position of Aethionema makes it an ideal reference for broader comparative genetics and genomics. To understand the evolution of Aethionema, and for a broader understanding of crucifer evolution, a time‐calibrated phylogenetic tree and biogeographical history of the genus is needed. METHODS:: Seventy‐six plastome coding regions and nuclear rDNA genes, mainly from herbarium material, covering 75% of all Aethionema species, were used to resolve a time‐calibrated Aethionema phylogeny. The different clades were characterized based on four morphological characters. The ancestral area of Aethionema was estimated with historical biogeographical analyses. KEY RESULTS:: Three well‐supported major clades within Aethionema were resolved. The ancestral area reconstruction and divergence‐time estimates are consistent with major dispersal events during the Pliocene from the Anatolian Diagonal. CONCLUSIONS:: We find that most Aethionema lineages originated along the Anatolian Diagonal, a floristic bridge connecting the east to the west, during the Pliocene. The dispersal of Aethionema correlates with the local geological events, such as the uplift of the Anatolian and Iranian plateaus and the formation of the major mountain ranges of the Irano‐Turanian region. Knowing the paleo‐ecological context for the evolution of Aethionema, in addition to the other lineages of Brassicaceae, facilitates our broader understanding for trait evolution and species diversification across the Brassicaceae. [ABSTRACT FROM AUTHOR]

PREMISE OF THE STUDY: Glucosinolates (GS) are a class of plant secondary metabolites that provide defense against herbivores and may play an important role in pollinator attraction. Through coevolution with plant-interacting organisms, glucosinolates have diversified into a variety of chemotypes through gene sub- and neofunctionalization. Polyploidy has been of major importance in the evolutionary history of these gene families and the development of chemically separate GS types. Here we study the effects of polyploidy in Tarenaya hassleriana (Cleomaceae) on the genes underlying GS biosynthesis. METHODS: We established putative orthologs of all gene families involved in GS biosynthesis through sequence comparison and their duplication method through calculation of synonymous substitution ratios, phylogenetic gene trees, and synteny comparison. We drew expression data from previously published work of the identified genes and compared expression in several tissues. KEY RESULTS: We show that the majority of gene family expansion in T. hassleriana has taken place through the retention of polyploid duplicates, together with tandem and transpositional duplicates. We also show that the large majority (>75%) is actively expressed either globally or in specific tissues. We show that MAM and CYP83 gene families, which are crucial to GS diversification in Brassicaceae, are also recruited into specific tissue expression pathways in Cleomaceae. CONCLUSIONS: Many GS genes have expanded through polyploidy, gene transposition duplication, and tandem duplication in Cleomaceae. Duplicate retention through these mechanisms is similar to A. thaliana, but based on the expression of GS genes, Cleomaceae-specific diversification of GS genes has taken place. [ABSTRACT FROM AUTHOR]

The ubiquitin-like modifier ( UBL) SUMO (Small Ubiquitin-Like Modifier) regulates protein function. Structural rather than sequence homology typifies UBL families. However, individual UBL types, such as SUMO, show remarkable sequence conservation. Selection pressure also operates at the SUMO gene copy number, as increased SUMO levels activate immunity and alter flowering time in Arabidopsis., We show how, despite this selection pressure, the SUMO family has diversified into eight paralogues in Arabidopsis. Relationships between the paralogues were investigated using genome collinearity and gene tree analysis. We show that palaeopolyploidy followed by tandem duplications allowed expansion and then diversification of the SUMO genes., For example, Arabidopsis SUMO5 evolved from the pan-eudicot palaeohexaploidy event (gamma), which yielded three SUMO copies. Two gamma copies were preserved as archetype SUMOs, suggesting subfunctionalization, whereas the third copy served as a hotspot for SUMO diversification., The Brassicaceae-specific alpha duplication then caused the duplication of one archetype gamma copy, which, by subfunctionalization, allowed the retention of both SUMO1 and SUMO2. The other archetype gamma copy was simultaneously pseudogenized ( SUMO4/6). A tandem duplication of SUMO2 subsequently yielded SUMO3 in the Brassicaceae crown group. SUMO3 potentially neofunctionalized in Arabidopsis, but it is lost in many Brassicaceae. Our advanced methodology allows the study of the birth and fixation of other paralogues in plants. [ABSTRACT FROM AUTHOR]

Chromosome rearrangements may result in both decrease and increase of chromosome numbers. Here we have used comparative chromosome painting ( CCP) to reconstruct the pathways of descending and ascending dysploidy in the genus Boechera (tribe Boechereae, Brassicaceae). We describe the origin and structure of three Boechera genomes and establish the origin of the previously described aberrant Het and Del chromosomes found in Boechera apomicts with euploid (2 n = 14) and aneuploid (2 n = 15) chromosome number. CCP analysis allowed us to reconstruct the origin of seven chromosomes in sexual B. stricta and apomictic B. divaricarpa from the ancestral karyotype ( n = 8) of Brassicaceae lineage I. Whereas three chromosomes ( BS4, BS6, and BS7) retained their ancestral structure, five chromosomes were reshuffled by reciprocal translocations to form chromosomes BS1- BS3 and BS5. The reduction of the chromosome number (from x = 8 to x = 7) was accomplished through the inactivation of a paleocentromere on chromosome BS5. In apomictic 2 n = 14 plants, CCP identifies the largely heterochromatic chromosome ( Het) being one of the BS1 homologues with the expansion of pericentromeric heterochromatin. In apomictic B. polyantha (2 n = 15), the Het has undergone a centric fission resulting in two smaller chromosomes - the submetacentric Het′ and telocentric Del. Here we show that new chromosomes can be formed by a centric fission and can be fixed in populations due to the apomictic mode of reproduction. [ABSTRACT FROM AUTHOR]

Development of chilling and freezing tolerance is complex and can be affected by photoperiod, temperature and photosynthetic performance; however, there has been limited research on the interaction of these three factors. We evaluated 108 recombinant inbred lines of B oechera stricta, derived from a cross between lines originating from Montana and Colorado, under controlled long day ( LD), short-day ( SD) and in an outdoor environment ( OE). We measured maximum quantum yield of photosystem II, lethal temperature for 50% survival and electrolyte leakage of leaves. Our results revealed significant variation for chilling and freezing tolerance and photosynthetic performance in different environments. Using both single- and multi-trait analyses, three main-effect quantitative trait loci ( QTL) were identified. QTL on linkage group ( LG)3 were SD specific, whereas QTL on LG4 were found under both LD and SD. Under all conditions, QTL on LG7 were identified, but were particularly predictive for the outdoor experiment. The co-localization of photosynthetic performance and freezing tolerance effects supports these traits being co-regulated. Finally, the major QTL on LG7 is syntenic to the Arabidopsis C-repeat binding factor locus, known regulators of chilling and freezing responses in A rabidopsis thaliana and other species. [ABSTRACT FROM AUTHOR]

Flooding events negatively affect plant performance and survival. Flooding gradients thereby determine the dynamics in vegetation composition and species abundance. In adaptation to flooding, the group VII Ethylene Response Factor genes ( ERF- VIIs) play pivotal roles in rice and A rabidopsis through regulation of anaerobic gene expression and antithetical survival strategies. We investigated if ERF- VIIs have a similar role in mediating survival strategies in eudicot species from flood-prone environments. Here, we studied the evolutionary origin and regulation of ERF- VII transcript abundance and the physiological responses in species from two genera of divergent taxonomic lineages ( R umex and R orippa). Synteny analysis revealed that angiosperm ERF- VIIs arose from two ancestral loci and that subsequent diversification and duplication led to the present ERF- VII variation. We propose that subtle variation in the regulation of ERF- VII transcript abundance could explain variation in tolerance among R orippa species. In R umex, the main difference in flood tolerance correlated with the genetic variation in ERF- VII genes. Large transcriptional differences were found by comparing the two genera: darkness and dark submergence-induced R umex ERF- VIIs, whereas HRE2 expression was increased in submerged R orippa roots. We conclude that the involvement of ERF- VIIs in flooding tolerance developed in a phylogenetic-dependent manner, with subtle variations within taxonomic clades. [ABSTRACT FROM AUTHOR]

The development of stress-tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans-)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives. [ABSTRACT FROM AUTHOR]

• Premise of the study: The evolution of asexual seed production (apomixis) from sexual relatives is a great enigma of plant biology. The genus Boechera is ideal for studying apomixis because of its close relation to Arabidopsis and the occurrence of sexual and apomictic species at low ploidy levels (diploid and triploid). Apomixis is characterized by three components: unreduced embryo-sac formation (apomeiosis). fertilization-independent embryogenesis (parthenogenesis), and functional endosperm formation (pseudogamy or autonomous endospermforntation). Understanding the variation in these traits within and between species has been hindered by the laborious histological analyses required to analyze large numbers of samples. • Methods: To quantify variability for the different components of apomictic seed development, we developed a high-throughput flow cytometric seed screen technique to measure embryo: endospeml ploidy in over 22000 single seeds derived from 71 accessions of diploid and triploid Boechera. • Key results: Three interrelated features were identified within and among Boechera species: (1) variation for most traits associated with apomictic seed formation, (2) three levels of apomeiosis expression (low, high, obligate), and (3) correlations between apomeiosis and parthenogenesis/pseudogamy. • Conclusions: The data presented here provide a framework for choosing specific genotypes for correlations with large "omits" data sets being collected for Boechera to study population structure, gene flow, and evolution of specific traits. We hypothesize that low levels of apomeiosis represent an ancestral condition of Boechera, whereas high apomeiosis levels may have been induced by global gene regulatory changes associated with hybridization. [ABSTRACT FROM AUTHOR]

• Understanding apomixis (asexual reproduction through seeds) is of great interest to both plant breeders and evolutionary biologists. The genus Boechera is an excellent system for studying apomixis because of its close relationship to Arabidopsis, the occurrence of apomixis at the diploid level, and its potentially simple inheritance by transmission of a heterochromatic ( Het) chromosome. • Diploid sexual Boechera stricta and diploid apomictic Boechera divaricarpa (carrying a Het chromosome) were crossed. Flow cytometry, karyotype analysis, genomic in situ hybridization, pollen staining and seed-production measurements were used to analyse the parents and resulting F1, F2 and selected F3 and test-cross (TC) generations. • The F1 plant was a low-fertility triploid that produced a swarm of aneuploid and polyploid F2 progeny. Two of the F2 plants were fertile near-tetraploids, and analysis of their F3 and TC progeny revealed that they were sexual and genomically stabilized. • The apomictic phenotype was not transmitted by genetic crossing as a single dominant locus on the Het chromosome, suggesting a complex genetic control of apomixis that has implications for future genetic and evolutionary analyses in this group. [ABSTRACT FROM AUTHOR]

Of the 340 genera in the Brassicaceae, apomictic reproduction is found only in the North American genus Boechera. We investigated phylogenetic relationships, ability to hybridize, mating system, and ploidy levels of 92 lines sampled from 85 populations and representing 19 Boechera species. Phylogenetic analyses based on chloroplast DNA sequences identified three lineages in the genus. Reciprocal crosses of each line were made to a common sexual diploid B. stricta tester. The resulting F3 progeny were analyzed for the inheritance of polymorphic microsatellite loci. genome size, and seed production. Intraspecific B. stricta crosses confirmed that this species is mostly diploid and sexual. Interspecific crosses revealed many other species were diploid and sexual and could be successfully hybridized with the tester. We also found obligate and facultative apomictic diploid and triploid lines. De novo F1 polyploids (either triploids or tetraploids) were derived from the union of nonreduced (from an apomictic parent) and reduced (from the tester) gametes. However, seed production of these F1 plants was generally low, suggesting a failure in the transmission of apomixis. The creation of a wide array of segregating genetic populations will facilitate future research on the evolution and inheritance of quantitative variation in Boechera. [ABSTRACT FROM AUTHOR]

Variation that arises in generations immediately following polyploidization may be important for the establishment, adaptation, and persistence of new polyploid species. We previously showed divergence for flowering time among lines from a resynthesized Brassica napus allopolyploid lineage derived from a cross of diploid B. rapa and B. oleracea. In this study, we more fully assess phenotypic differentiation of lines from the previously studied lineage and of lines derived from an additional resynthesized B. napus lineage. Nine polyploid lines and their diploid parents were grown under four growth conditions and measured for eight life-history traits. Polyploid lines within a lineage were expected to be genetically identical because they were derived from individual, chromosome-doubled amphihaploid plants. However, significant differences were found among lines within lineages for every phenotypic trait measured and in response to different growth conditions (genotype by environment interactions). When phenotypes of each polyploid line for each trait in each environment were compared with their diploid progenitors, approximately 30% were like one or the other parent, 50% were intermediate, and 20% were transgressive. Our results demonstrate extensive de novo variation in new polyploid lineages. Such changes could contribute to the evolutionary potential in naturally occurring polyploids. [ABSTRACT FROM AUTHOR]